Re: [modeller_usage] Regarding manual protein sequence alignment

["Luis Rosales" <>]

Hi all,

Mmmm...

Let me kow if I am wrong about this, but as far as I can say the problem with
stereochemistry (Ramachandran plot) is not necessarily related to a bad
sequence alignment... 
 
(You could have a very bad stereochem [maybe as a result of a bad/poorly
refined model] and a good rama plot. Modeller is more suceptible to give you
the inverse scenario: a really good stereochem, without regard of the quality
of your alignment...)

there are several tools more suited to evaluate your alignment and as a
result, your coordinate asssignment (they evaluate the coordinates of your
final model). 

I think that Prosa2003 and profile3D are a couple of examples.

Hope this helps,

Luis

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---------- Original Message -----------
From: rajesh rengaraj <>
To: inbios groups <>, modeller
<>, groups mtech <>
Sent: Tue, 15 Mar 2005 09:00:59 +0000 (GMT)
Subject: [modeller_usage] Regarding manual protein sequence alignment

> Hi friends.
> 
>    I need help from our groups regarding the Protein
> manual sequence alignment.I modelled a protein which
> shows low Ramachandran plot validatity in order to
> increase this i have to do the manual alignment.I dont
> know what are the procedure for this and how to do
> this, whether it is depends upon the physico-chemical
> properties of amino acids or any other else.
> 
>       So Kindly do the needful.
> 
>              Take care.
> 
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------- End of Original Message -------